+Open data
-Basic information
Entry | Database: PDB / ID: 7oku | ||||||
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Title | X-ray structure of soluble EPCR in P3121 space group | ||||||
Components | Endothelial protein C receptor | ||||||
Keywords | LIPID BINDING PROTEIN / MHC class I-like / phospholipid / anticoagulant / endothelial cell membrane receptor | ||||||
Function / homology | Function and homology information negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Erausquin, E. / Dichiara, M.G. / Lopez-Sagaseta, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Identification of a broad lipid repertoire associated to the endothelial cell protein C receptor (EPCR). Authors: Erausquin, E. / Moran-Garrido, M. / Saiz, J. / Barbas, C. / Dichiara-Rodriguez, G. / Urdiciain, A. / Lopez-Sagaseta, J. #1: Journal: Biorxiv / Year: 2021 Title: A novel alpha / beta T-cell subpopulation defined by recognition of EPCR Authors: Erausquin, E. / Moran-Garrido, M. / Saiz, J. / Barbas, C. / Dichiara-Rodriguez, G. / Ramirez, N. / Lopez-Sagaseta, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oku.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oku.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 7oku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/7oku ftp://data.pdbj.org/pub/pdb/validation_reports/ok/7oku | HTTPS FTP |
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-Related structure data
Related structure data | 7oksC 7oktC 7okvC 1lqvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22200.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Homo sapiens (human) / Gene: PROCR, EPCR / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNN8 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 56 molecules
#4: Chemical | #5: Chemical | ChemComp-PTY / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.0 M Sodium formate, 0.1 M Sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2020 |
Radiation | Monochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.12 Å / Num. obs: 21046 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 52.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071 / Χ2: 0.91 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1463 / CC1/2: 0.516 / Χ2: 0.78 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LQV Resolution: 1.95→38.09 Å / SU ML: 0.2984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0911 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→38.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 25.8797007934 Å / Origin y: -19.3138883521 Å / Origin z: 3.43537806534 Å
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Refinement TLS group |
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